[gmx-users] T-coupling of water and ion
feenstra at few.vu.nl
Tue May 31 13:05:40 CEST 2005
Jian Zou wrote:
> I just generate 8 ADE, dissolve it in a water box, run EM, PR, then MD.
> Therefore, the starting structure is taken from the PR-MD result.
And which ref_t did you use during PR-MD?
> This sounds reasonable to me.
> But I'm still wondering why couple Na seperately will give the
> temperature for RNA 100 degree C lower than the ref_t.
Your *whole* system is (far) below the 400K ref_t. I can't see how your
.mdp file could have produced these results. Are you sure these are the
settings you used? Perhaps you can check your .tpr file or md.log (or
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